Publications by authors named "Vendula Valásková"

11 Publications

  • Page 1 of 1

Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood.

Int J Syst Evol Microbiol 2012 Jul 19;62(Pt 7):1512-1520. Epub 2011 Aug 19.

S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia.

Two strains of subdivision 1 Acidobacteria, a pink-pigmented bacterium KA1(T) and a colourless isolate WH120(T), were obtained from acidic Sphagnum peat and wood under decay by the white-rot fungus Hyploma fasciculare, respectively. Cells of these isolates were Gram-negative-staining, non-motile, short rods, which were covered by large polysaccharide capsules and occurred singly, in pairs, or in short chains. Strains KA1(T) and WH120(T) were strictly aerobic mesophiles that grew between 10 and 33 °C, with an optimum at 22-28 °C. Both isolates developed under acidic conditions, but strain WH120(T) was more acidophilic (pH growth range 3.5-6.4; optimum, 4.0-4.5) than strain KA1(T) (pH growth range 3.5-7.3; optimum , 5.0-5.5). The preferred growth substrates were sugars. In addition, the wood-derived isolate WH120(T) grew on oxalate, lactate and xylan, while the peat-inhabiting acidobacterium strain KA1(T) utilized galacturonate, glucuronate and pectin. The major fatty acids were iso-C(15:0) and iso-C(17:1)ω8c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid. The quinone was MK-8. The DNA G+C contents of strains KA1(T) and WH120(T) were 54.1 and 51.7 mol%, respectively. Strains KA1(T) and WH120(T) displayed 97.8% 16S rRNA gene sequence similarity to each other. The closest recognized relatives were Acidobacterium capsulatum and Telmatobacter bradus (93.4-94.3% 16S rRNA gene sequence similarity). These species differed from strains KA1(T) and WH120(T) by their ability to grow under anoxic conditions, the absence of capsules, presence of cell motility and differing fatty acid composition. Based on these differences, the two new isolates are proposed as representing a novel genus, Acidicapsa gen. nov., and two novel species. Acidicapsa borealis gen. nov., sp. nov. is the type species for the new genus with strain KA1(T) (=DSM 23886(T)=LMG 25897(T)=VKM B-2678(T)) as the type strain. The name Acidicapsa ligni sp. nov. is proposed for strain WH120(T) (=LMG 26244(T)=VKM B-2677(T)=NCCB 100371(T)).
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http://dx.doi.org/10.1099/ijs.0.034819-0DOI Listing
July 2012

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition.

ISME J 2012 Feb 21;6(2):248-58. Epub 2011 Jul 21.

Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Vídeňská, Praha, Czech Republic.

Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.
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http://dx.doi.org/10.1038/ismej.2011.95DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260513PMC
February 2012

Development of bacterial community during spontaneous succession on spoil heaps after brown coal mining.

FEMS Microbiol Ecol 2011 Oct 21;78(1):59-69. Epub 2011 Jul 21.

Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Praha, Czech Republic.

Changes in the abundance of bacteria and fungi and in the composition of bacterial communities during primary succession were investigated in a brown coal mine deposit area near Sokolov, the Czech Republic, using phospholipid fatty acids analysis, microarray and 16S rRNA gene sequencing. The study considered a chronosequence of sites undergoing spontaneous succession: 6-, 12-, 21- and 45-year-old and a 21-year-old site revegetated with Alnus glutinosa. During succession, organic carbon and the total nitrogen content increased while the pH and the C/N ratio decreased. Microbial biomass and bacterial diversity increased until 21 years and decreased later; bacteria dominated over fungi in the initial and late phases of succession. Bacterial community composition of the 6-year-old site with no vegetation cover largely differed from the older sites, especially by a higher content of Gammaproteobacteria, Cyanobacteria and some Alphaproteobacteria. Bacteria belonging to the genera Acidithiobacillus, Thiobacillus and related taxa, the CO(2) and N(2) fixers, dominated the community at this site. In the later phases, bacterial community development seemed to reflect more the changes in soil nutrient content and pH than vegetation with a decrease of Actinobacteria and an increase of Acidobacteria. The site revegetated with A. glutinosa resembled the 45-year-old primary succession site and exhibited an even lower pH and C/N ratio, indicating that recultivation is able to accelerate soil development.
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http://dx.doi.org/10.1111/j.1574-6941.2011.01164.xDOI Listing
October 2011

Saprotrophic basidiomycete mycelia and their interspecific interactions affect the spatial distribution of extracellular enzymes in soil.

FEMS Microbiol Ecol 2011 Oct 26;78(1):80-90. Epub 2011 May 26.

Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Prague, Czech Republic.

Saprotrophic cord-forming basidiomycetes are important decomposers of lignocellulosic substrates in soil. The production of extracellular hydrolytic enzymes was studied during the growth of two saprotrophic basidiomycetes, Hypholoma fasciculare and Phanerochaete velutina, across the surface of nonsterile soil microcosms, along with the effects of these basidiomycetes on fungi and bacteria within the soil. Higher activities of α-glucosidase, β-glucosidase, cellobiohydrolase, β-xylosidase, phosphomonoesterase and phosphodiesterase, but not of arylsulphatase, were recorded beneath the mycelia. Despite the fact that H. fasciculare, with exploitative hyphal growth, produced much denser hyphal cover on the soil surface than P. velutina, with explorative growth, both fungi produced similar amounts of extracellular enzymes. In the areas where the mycelia of H. fasciculare and P. velutina interacted, the activities of N-acetylglucosaminidase, α-glucosidase and phosphomonoesterase, the enzymes potentially involved in hyphal cell wall damage, and the utilization of compounds released from damaged hyphae of interacting fungi, were particularly increased. No significant differences in fungal biomass were observed between basidiomycete-colonized and noncolonized soil, but bacterial biomass was reduced in soil with H. fasciculare. The increases in the activities of β-xylosidase, β-glucosidase, phosphomonoesterase and cellobiohydrolase with increasing fungal:bacterial biomass ratio indicate the positive effects of fungal enzymes on nutrient release and bacterial abundance, which is reflected in the positive correlation of bacterial and fungal biomass content.
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http://dx.doi.org/10.1111/j.1574-6941.2011.01123.xDOI Listing
October 2011

Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition.

FEMS Microbiol Ecol 2011 Feb 26;75(2):291-303. Epub 2010 Nov 26.

Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Prague, Czech Republic.

The links among the changes in litter chemistry, the activity of extracellular enzymes and the microbial community composition were observed in Quercus petraea litter. Three phases of decomposition could be distinguished. In the early 4-month stage, with high activities of β-glucosidase, β-xylosidase and cellobiohydrolase, 16.4% of litter was decomposed. Hemicelluloses were rapidly removed while cellulose and lignin degradation was slow. In months 4-12, with high endocellulase and endoxylanase activities, decomposition of cellulose prevailed and 31.8% of litter mass was lost. After the third phase of decomposition until month 24 with high activity of ligninolytic enzymes, the litter mass loss reached 67.9%. After 2 years of decay, cellulose decomposition was almost complete and most of the remaining polysaccharides were in the form of hemicelluloses. Fungi largely dominated over bacteria as leaf endophytes and also in the litter immediately before contact with soil, and this fungal dominance lasted until month 4. Bacterial biomass (measured as phospholipid fatty acid content) in litter increased with time but also changed qualitatively, showing an increasing number of Actinobacteria. This paper shows that the dynamics of decomposition of individual litter components changes with time in accordance with the changes in the microbial community composition and its production of extracellular enzymes.
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http://dx.doi.org/10.1111/j.1574-6941.2010.00999.xDOI Listing
February 2011

Effect of long-term preservation of basidiomycetes on perlite in liquid nitrogen on their growth, morphological, enzymatic and genetic characteristics.

Fungal Biol 2010 Nov-Dec;114(11-12):929-35. Epub 2010 Sep 17.

Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.

The macro- and micro-morphological features, mycelial extension rate, enzymatic activities and possible genetic changes were studied in 30 selected strains of basidiomycetes after 10-year cryopreservation on perlite in liquid nitrogen (LN). Comparisons with the same strains preserved by serial transfers on nutrient media at 4°C were also conducted. Production of ligninolytic enzymes and hydrogen peroxide was studied by quantitative spectrophotometric methods, whereas semiquantitative API ZYM testing was used to compare the levels of a wide range of hydrolytic enzymes. Our results show that cryopreservation in LN did not cause morphological changes in any isolate. The vitality of all fungi was successfully preserved and none of the physiological features were lost, even though the extension rate and enzyme activity were slightly affected. Moreover, sequence analysis of eight strains did not detect any changes in their genetic features after cryopreservation. These findings suggest that the perlite-based freezing protocol is suitable for long-term preservation of large numbers of basidiomycetes.
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http://dx.doi.org/10.1016/j.funbio.2010.08.009DOI Listing
February 2011

Phylogenetic composition and properties of bacteria coexisting with the fungus Hypholoma fasciculare in decaying wood.

ISME J 2009 Oct 11;3(10):1218-21. Epub 2009 Jun 11.

Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Prague 4 14220, Czech Republic.

White-rot fungi are major degraders of woody materials in terrestrial environments because of their ability to decompose lignin. However, little is known on the possible associations of white-rot fungi with other microorganisms during wood decay. We investigated the numbers, community composition and functional traits of bacteria present in natural wood samples under advanced decay by the white-rot basidiomycete Hypholoma fasciculare. The wood samples contained high numbers of cultivable bacteria (0.2-8 x 10(9) colony forming units (CFU) per g of dry wood). Most cultivable bacteria belonged to Proteobacteria and Acidobacteria (75% and 23% of sequences, respectively). The same phyla were also found to be dominant (59% and 23%, respectively) using a non-culturable quantification technique, namely, direct cloning and sequencing of 16sRNA genes extracted from wood. Bacteria that could be subcultured consisted of acid-tolerant strains that seemed to rely on substrates released by lignocellulolytic enzyme activities of the fungus. There were no indications for antagonism (antibiosis) of the bacteria against the fungus.
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http://dx.doi.org/10.1038/ismej.2009.64DOI Listing
October 2009

Degradation of cellulose by basidiomycetous fungi.

FEMS Microbiol Rev 2008 May 26;32(3):501-21. Epub 2008 Mar 26.

Laboratory of Biochemistry of Wood-Rotting Fungi, Institute of Microbiology of the ASCR v.v.i., Vídenská 1083, Prague 4, Czech Republic.

Cellulose is the main polymeric component of the plant cell wall, the most abundant polysaccharide on Earth, and an important renewable resource. Basidiomycetous fungi belong to its most potent degraders because many species grow on dead wood or litter, in environment rich in cellulose. Fungal cellulolytic systems differ from the complex cellulolytic systems of bacteria. For the degradation of cellulose, basidiomycetes utilize a set of hydrolytic enzymes typically composed of endoglucanase, cellobiohydrolase and beta-glucosidase. In some species, the absence of cellobiohydrolase is substituted by the production of processive endoglucanases combining the properties of both of these enzymes. In addition, systems producing hydroxyl radicals based on cellobiose dehydrogenase, quinone redox cycling or glycopeptide-based Fenton reaction are involved in the degradation of several plant cell wall components, including cellulose. The complete cellulolytic complex used by a single fungal species is typically composed of more than one of the above mechanisms that contribute to the utilization of cellulose as a source of carbon or energy or degrade it to ensure fast substrate colonization. The efficiency and regulation of cellulose degradation differs among wood-rotting, litter-decomposing, mycorrhizal or plant pathogenic fungi and yeasts due to the different roles of cellulose degradation in the physiology and ecology of the individual groups.
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http://dx.doi.org/10.1111/j.1574-6976.2008.00106.xDOI Listing
May 2008

Degradation of cellulose and hemicelluloses by the brown rot fungus Piptoporus betulinus--production of extracellular enzymes and characterization of the major cellulases.

Microbiology (Reading) 2006 Dec;152(Pt 12):3613-3622

Laboratory of Biochemistry of Wood-Rotting Fungi, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague 4, Czech Republic.

Piptoporus betulinus is a common wood-rotting fungus parasitic for birch (Betula species). It is able to cause fast mass loss of birch wood or other lignocellulose substrates. When grown on wheat straw, P. betulinus caused 65% loss of dry mass within 98 days, and it produced endo-1,4-beta-glucanase (EG), endo-1,4-beta-xylanase, endo-1,4-beta-mannanase, 1,4-beta-glucosidase (BG), 1,4-beta-xylosidase, 1,4-beta-mannosidase and cellobiohydrolase activities. The fungus was not able to efficiently degrade crystalline cellulose. The major glycosyl hydrolases, endoglucanase EG1 and beta-glucosidase BG1, were purified. EG1 was a protein of 62 kDa with a pI of 2.6-2.8. It cleaved cellulose internally, produced cellobiose and glucose from cellulose and cellooligosaccharides, and also showed beta-xylosidase and endoxylanase activities. The K(m) for carboxymethylcellulose was 3.5 g l(-1), with the highest activity at pH 3.5 and 70 degrees C. BG1 was a protein of 36 kDa with a pI around 2.6. It was able to produce glucose from cellobiose and cellooligosaccharides, but also produced galactose, mannose and xylose from the respective oligosaccharides and showed some cellobiohydrolase activity. The K(m) for p-nitrophenyl-1,4-beta-glucoside was 1.8 mM, with the highest activity at pH 4 and 60 degrees C, and the enzyme was competitively inhibited by glucose (K(i)=5.8 mM). The fungus produced mainly beta-glucosidase and beta-mannosidase activity in its fruit bodies, while higher activities of endoglucanase, endoxylanase and beta-xylosidase were found in fungus-colonized wood.
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http://dx.doi.org/10.1099/mic.0.29149-0DOI Listing
December 2006

Estimation of bound and free fractions of lignocellulose-degrading enzymes of wood-rotting fungi Pleurotus ostreatus, Trametes versicolor and Piptoporus betulinus.

Res Microbiol 2006 Mar 8;157(2):119-24. Epub 2005 Aug 8.

Laboratory of Biochemistry of Wood-Rotting Fungi, Institute of Microbiology ASCR, Vídenská 1083, 14220 Praha 4, Czech Republic.

Liquid cultures with cellulose and solid state fermentation cultures on wheat straw of the white-rot fungi Pleurotus ostreatus and Trametes versicolor and the brown-rot fungus Piptoporus betulinus were assayed for the free and solid fraction-bound activity of lignocellulose-degrading enzymes. The majority of the ligninolytic enzymes laccase and Mn peroxidase was detected in the free fraction of P. ostreatus and T. versicolor. The endocleaving enzymes endo-1,4-beta-glucanase, endo-1,4-beta-mannanase and endo-1,4-beta-xylanase were detected almost exclusively in the free fraction, while significant amounts of 1,4-beta-glucosidase, cellobiohydrolase, 1,4-beta-xylosidase and 1,4-beta-mannosidase were present in the bound fraction depending on the mode of cultivation and the species. The bound enzymes accounted for 66% of the total activity in P. ostreatus straw cultures, 35% in T. versicolor and only 8% in P. betulinus. The enzymes also showed significant differences in freeze-drying stability. Hydrolases in general showed high stability, whereas laccase and Mn peroxidase of P. ostreatus were the least stable.
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http://dx.doi.org/10.1016/j.resmic.2005.06.004DOI Listing
March 2006

Degradation of lignocellulose by Pleurotus ostreatus in the presence of copper, manganese, lead and zinc.

Res Microbiol 2005 Jun-Jul;156(5-6):670-6. Epub 2005 Apr 12.

Laboratory of Biochemistry of Wood-Rotting Fungi, Institute of Microbiology ASCR, Vídenská 1083, 14220 Prague 4, Czech Republic.

Pleurotus ostreatus produces the cellulolytic and hemicellulolytic enzymes endo-1,4-beta-glucanase, exo-1,4-beta-glucanase, 1,4-beta-glucosidase, endo-1,4-beta-xylanase, 1,4-beta-xylosidase, endo-1,4-beta-mannanase and 1,4-beta-mannosidase and ligninolytic enzymes Mn-peroxidase and laccase during growth on wheat straw in the presence and absence of Cu, Mn, Pb, and Zn. This is the first report concerning endo-1,4-beta-mannanase in P. ostreatus. Although the concentrations of trace metals in wheat straw ranged from units to tens of microg g(-1), only 3-6% (Fe, Pb) or 30-45% (Cu, Mn, Zn) of the total amount was extractable and available for the fungus. The substrate colonization rate was only decreased by high concentrations of Cu and Zn; the loss of dry mass differed among treatments in the initial phase of fungal growth, and at the end of the experiment (day 98) it was significantly lower in metal-containing treatments (63-66%) than in the control (70%). The cellulolytic and hemicellulolytic enzyme were prone to a metal effect except for the increase in endo-1,4-beta-glucanase and 1,4-beta-glucosidase in the presence of Zn. Laccase activity was increased by all tested metals, and unlike other white-rot fungi, Mn-peroxidase levels were low in the presence of manganese.
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http://dx.doi.org/10.1016/j.resmic.2005.03.007DOI Listing
October 2005